About this Research Topic
Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, systematic worldwide studies of these dense, human microbial ecosystems are still lacking. The recent efforts to address this gap by the MetaSUB International Consortium have constituted a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, highlighted potential forensic applications, and provided an essential first draft of the global antimicrobial resistance (AMR) burden of the world’s cities.
This is, however, just the first step, and the scientific community now has a unique opportunity to push the state-of-the-art in methodology development for sample collection and processing as well as further data generation, analysis, and understanding. The quantum leap can be done by building on this rich dataset as well as extending it by combining with data from neighbouring efforts (e.g., Earth Microbiome Project) or other studies. All this would allow unveiling the metagenomic world of the human-built environment and may pave the way to building smart cities where the management of the microbiota can be achieved.
Understanding this complex, pervasive, and medically impactful microbial world is especially crucial in the context of the ongoing SARS-CoV-2 pandemic. Understanding microbial behaviour and driving factors, together with the possibility of measuring and analysing in ‘near real time,’ would allow us to monitor or even predict the pathogen spread, support first responders’ efforts, and defend against future pandemics. In this sense, the constant monitoring of the environmental microbiota may be a pivotal step towards a safer world through metagenomics surveillance.
Environmental metagenomics has also a new application in biogeography as well as in intelligence. The future of DNA-based forensic methods is in the development of data science approaches to predict sample origin based on its metagenomics profile. The application of new technologies raises, however, technical challenges and requires careful ethical consideration.
The scope of this Research Topic should span manuscripts addressing questions about methodological advancements both in metagenomic data generation as well as analysis, in addition to a focus on data exploration. In particular, we would be interested in manuscripts addressing:
• Methodological developments for urban microbiome sample collection
• Methodological developments for low material DNA/RNA extraction protocols
• Methodological developments for urban microbiome short-/long-read Whole Metagenome Sequencing
• Metagenomics data analysis approaches for species identification and quantification
• Data analysis approaches for identification of common as well as specific species in the context of location-specific meta-data
• Application of microbial biodiversity to biogeography, pathogen distribution/spreading for disease monitoring
• Application of the metagenomics approach in intelligence and forensics
• Studies on the complementarity of surface and air microbiome in public spaces
• Annotating unknown microbial species and unveiling their function
• Antibiotic resistance profiling of urban microbiome
Keywords: urban microbiome, whole metagenomic sequencing, antimicrobial resistance, biogeography
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.